2exa

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (00:54, 21 November 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2exa.png|left|200px]]
 
-
<!--
+
==Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with FAROM==
-
The line below this paragraph, containing "STRUCTURE_2exa", creates the "Structure Box" on the page.
+
<StructureSection load='2exa' size='340' side='right'caption='[[2exa]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[2exa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EXA FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGF:(2R,5R)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-5-[(2R)-TETRAHYDROFURAN-2-YL]-2,5-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLIC+ACID'>DGF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-
{{STRUCTURE_2exa| PDB=2exa | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2exa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exa OCA], [https://pdbe.org/2exa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2exa RCSB], [https://www.ebi.ac.uk/pdbsum/2exa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2exa ProSAT]</span></td></tr>
 +
</table>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ex/2exa_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2exa ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The crystal structure of penicillin binding protein 4 (PBP4) from Escherichia coli, which has both DD-endopeptidase and DD-carboxypeptidase activity, is presented. PBP4 is one of 12 penicillin binding proteins in E. coli involved in the synthesis and maintenance of the cell wall. The model contains a penicillin binding domain similar to known structures, but includes a large insertion which folds into domains with unique folds. The structures of the protein covalently attached to five different antibiotics presented here show the active site residues are unmoved compared to the apoprotein, but nearby surface loops and helices are displaced in some cases. The altered geometry of conserved active site residues compared with those of other PBPs suggests a possible cause for the slow deacylation rate of PBP4.
-
===Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with FAROM===
+
Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics.,Kishida H, Unzai S, Roper DI, Lloyd A, Park SY, Tame JR Biochemistry. 2006 Jan 24;45(3):783-92. PMID:16411754<ref>PMID:16411754</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 2exa" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_16411754}}, adds the Publication Abstract to the page
+
*[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 16411754 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_16411754}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
2EXA is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXA OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:16411754</ref><references group="xtra"/>
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Kishida, H.]]
+
[[Category: Large Structures]]
-
[[Category: Lloyd, A.]]
+
[[Category: Kishida H]]
-
[[Category: Park, S Y.]]
+
[[Category: Lloyd A]]
-
[[Category: Roper, D I.]]
+
[[Category: Park S-Y]]
-
[[Category: Tame, J R.H.]]
+
[[Category: Roper DI]]
-
[[Category: Unzai, S.]]
+
[[Category: Tame JRH]]
-
[[Category: D-alanyl-d-alanine-carboxypeptidase]]
+
[[Category: Unzai S]]
-
[[Category: D-alanyl-d-alanine-endopeptidase]]
+
-
[[Category: Farom]]
+
-
[[Category: Penem]]
+
-
[[Category: Penicillin,cephem]]
+
-
[[Category: Penicillin-binding protein]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 10:08:06 2009''
+

Current revision

Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with FAROM

PDB ID 2exa

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2exa"
Personal tools